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Provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB is a functional genomic database for Plasmodium spp. It belongs to a family of genomic resources that are housed under the EuPathDB Bioinformatics Resource Center (BRC) umbrella. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page.
CGD / Cucurbit Genomics Database
A database which offers gene annotation of cucurbit. This base offers the genome of Melon (Cucumis melo), Cucumber (Cucumis sativus), Watermelon (Citrullus lanatus), Pumpkin (Cucurbita maxima). The Cucurbitaceae consist of 98 proposed genera with 975 species, mainly in regions tropical and subtropical. All species are sensitive to frost. Most of the plants in this family are annual vines, but some are woody lianas, thorny shrubs, or trees (Dendrosicyos). Cucurbit belongs to the Cucurbitaceae family.
Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge.
A genomic database for Giardia lamblia. GiardiaDB is based on the genome of the WBC6 clinical isolate of G. lamblia. It is accessed via the standard EuPathDB web interface, providing a wide variety of tools for genomic database mining. In addition to BLAST and pattern/motif similarity searches, users can identify genes based on genomic position; common name or keyword; gene attributes (such as gene type, or number of exons); evidence of transcript expression including ESTs, SAGE tags, microarray and proteomics; gene product annotation (such as GO function, or EC enzyme number); and predicted cellular location (based on signal peptide and transmembrane predictions).
Stores raw and cleans expressed sequence tag (EST) classified in EST division of GenBank (dbEST) libraries. CleanEST is a web-based database server that provides two different cleansed sequences for each dbEST library: “pre-cleansed” and “user-cleansed”. The database uses an automatic user-cleansing pipeline, in which sequences in a user-selected library are cleansed on-the-fly according to user-input options. Four types of search menus are available: organism, sequencing center, eVOC ontologies (for human libraries) and user sequences.
tomatEST / Tomato Expressed Sequence Tag
Supports investigations on expressed sequence data from multiple tomato species. tomatEST is a database of expressed sequence tag (EST) /complementary DNA (cDNA) sequences from dbEST libraries, a division of GenBank containing sequence data. This resource was developed to provide a workbench for mining the complexity of EST sequence information content from multiple tomato species (i) for expression pattern analysis and (ii) for gene discovery in the framework of Solanum lycopersicum genome project.
CR-EST / CRop EST database
Provides access to sequence, classification, clustering and annotation data of crop EST projects. CR-EST currently holds more than 200,000 sequences derived from 48 cDNA libraries of six species: barley, wheat, pea, petunia, tobacco and potato. The barley section comprises approximately one-third of all publicly available ESTs. CR-EST deploys an automatic EST preparation pipeline that includes the identification of chimeric clones in order to transparently display the data quality. Sequences are clustered in species-specific projects to currently generate a non-redundant set of approximately 45,000 consensus sequences.
Hosts a comprehensive collection of Orchidaceae floral transcriptomes. The OrchidBase is a collection of 37,979,342 sequence reads collected from 11 in-house Phalaenopsis orchid cDNA libraries. Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-generation sequencing (NGS) including both Roche 454 and Solexa Illumina sequencers. These reads were assembled into 8,501 contigs and 76,116 singletons, resulting in 84,617 non-redundant transcribed sequences with an average length of 459 bp. The Orchidbase provides a detailed annotation including general information, relative expression level, gene ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway mapping and gene network prediction. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded.
Provides a repository for silkworm genome information for functional and applied genomics, including data from KAIKO2DDB of proteome data, Bombyx trap database for transgene and reporter data. KAIKOcDNA compiles genomic sequences, map information and expressed sequence tags (EST) data. The database makes available 4 map viewers: gene viewer, sequence search, keyword and position search systems. Results can be visualized at the level of nucleotide sequence, gene, scaffold and chromosome.
Stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, Pleurochrysome also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes.
BDGP / Berkeley Drosophila Genome Project
Provides sequence of euchromatic genome of Drosophila melanogaster in high quality. BDGP is a resource developed to (i) produce gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans, (ii) characterize sequence and expression of cDNAs and (iii) develop informatics tools that support the experimental process, identify features of DNA sequence, and allow to present up-to-date information about annotated sequence to the research community.
PIP / Potential Intron Polymorphism
Provides access to information about potential intron polymorphism (PIP) markers and homologous relationships among PIP markers from different plant species. PIP contains more than 55,000 PIP markers for about 60 plant species. Users can search the database by (i) species name, (ii) marker ID, (iii) gene name in subject species, (iv) PlantGDB PUT ID, (v) intron length range in subject species, (vi) Gene Ontology (GO) number in subject species and (vii) gene description in subject species.
LSD / Littorina sequence database
Facilitates genome research in Littorina saxatilis and related species. LSD was built by operating a hybrid assembly between four different expressed sequence tag (EST) data sets: two based on Sanger sequencing and two based on 454 sequencing. It can be useful to find markers such as microsatellites, single nucleotide polymorphisms (SNPs) useful for studies of population structure and phylogeny, and for genetic mapping and population genomic approaches.
SABRE2 / Systematic consolidation of Arabidopsis and other Botanical Resources
Cross-searches plant genetic resources through publicly available Arabidopsis information. In SABRE, plant expressed sequence tag (EST)/cDNA clones are related to TAIR (The Arabidoposis Information Resource) gene models and their annotations through sequence similarity. By entering a keyword, SABRE searches and retrieves TAIR gene models and annotations, together with homologous gene clones from various plant species. SABRE thus facilitates using TAIR annotations of Arabidopsis genes for research on homologous genes from other model plants.
Handles both microarray expression data and sequence assembly and annotation data. ANEXdb is an open-source web application that supports integrated access of two databases that house microarray expression (ExpressDB) and EST annotation (AnnotDB) data. Although ANEXdb currently houses porcine-specific data, it has been designed to be species independent. ANEXdb can be easily customized for other species by populating the databases with the relevant annotation and expression data from a variety of platforms such as Affymetrix GeneChips in other species or custom arrays.
Provides a unified view of the human transcriptome. WikiCell is an open and public platform dedicated to the annotation of the human transcriptome. Researchers can contribute transcriptome data, including ESTs and annotations. The wiki format allows authors to create and edit any number of interlinked webpages. Based on the anatomy of the human body, the logical structure traces out an image of refined classification from nine major systems to cell level, and includes both physiological and pathological transcriptome data. WikiCell can be searched by organ, tissue, and cell type, as well as GenBank accession number.

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